Rational design of peptides with antimicrobial activity against the pathogenic bacterium Pseudomonas aeruginosa

TUMAS IGNACIO; MIGUEL VIRGINIA; MONTI MARIELA R

Congreso; XLIX Reunión Anual de SAB; 2021

The Gram-negative bacterium Pseudomonas aeruginosa (PA) is an opportunistic pathogen capable of producing different infections. It has a marked tendency to acquire resistance to antibiotics for clinical use. It is among the main bacteria with priority for the development of new antimicrobials, according to the WHO. We propose as a new strategy the in silico development of peptides whose mechanism of action consists of interrupting protein-protein interactions (PPI) vital for PA. With this purpose, we have focused on the node proteins that participate in fundamental processes for the survival of the bacteria. The periplasmic protein TolB was chosen as a target, since it participates in the division and transport of other proteins through the PA membrane. Its essential role has been demonstrated in the literature and there are several crystalline structures of its homologue in E.coli alone (1C5K and 1CRZ) or interacting with one of its interaction pairs, such as PAL protein (2HQS and 2W8B) and colicin fragments ( 2IVZ, 3IAX and 4JML). We generated a TolB model of PA using MODELLER and a multi-template homology modeling approach. This model was used to build four different TOLB-partners complexes using PAL, and three colicines as partners, resulting in 4 different protein-protein structures. These complexes were used as starting points for 30 ns molecular dynamics simulations (DM) in order to evaluate if the complex remains stable. Also, we determined the energy contribution of the residues of the ligands in the interaction with TolB using GROMACS. We found that the complexes showed low RMSD values and high affinity energies demonstrating that PAL and the colicins fragments can interact with TolB of PA. Finally, we designed various 10 amino acid length peptides that mimics the interaction of PAL and colicins using the residues that showed the stronger affinity with TolB of PA and we performed a virtual screening of them by docking using the Autodock CrankPep program.